Physiology of Microorganisms Lecture 1 PDF

# Lecture 1: Physiology of Microorganisms - Exploring all metabolic and physiological pathways of microorganisms. ## Media and Microbial Growth - Media -> Microorganisms - Growth of Microorganisms: - Increase in cell biomass - Increase in cell number - Physiology: understanding the mecha...

# Lecture 1: Physiology of Microorganisms - Exploring all metabolic and physiological pathways of microorganisms. ## Media and Microbial Growth - Media -> Microorganisms - Growth of Microorganisms: - Increase in cell biomass - Increase in cell number - Physiology: understanding the mechanisms of microbial growth ## Media for Growing Fungi - Fungi contain: - Glucose (growth source) - Yeast extract or NaNO2 - MgSO4 - K2HPO4 - Micro-elements ## Composing Cell Biomass - **Polymers**: - Sugars - Starch - Cellulose - DNA - Protein - RNA **Note**: - The sugar resulted from microbial growth. - Chitin is the main component of fungal cell walls. - Cellulose is one of the most main components in most microorganisms. ## Enzymes - Natural proteins that accelerate or inactivate reactions by decreasing the energy required for the reaction. ## Enzyme Structure - **Holoenzyme:** - Protein (Apoenzyme) - Non-protein (Co-factor or Co-enzyme): - Metaloenzyme (metals like Cu, Fe, Zn) - Organic: - Vitamins - Fats - FAD, NAD - Heme - **The only case where enzymes don't compose from protein or contain only a low amount of protein is:** - **Ribozyme:** mainly RNA + few amount of protein. ## Enzyme Formation - **DNA** -> **Transcription** -> **RNA** -> **Translation** -> **Protein** ## Steps of Enzyme Maturation - **Start codon (AUG):** - Simple, encoding the protein - First amino acid is methionine - U terminal contains ammonia for methionine - **Maturation (Processing):** - Highly active enzyme ## Classification of Enzymes - Based on the International Union of Biochemistry (IUB). - Enzymes are classified into 6 categories based on 3 features: - Amino acid sequence - Sterio structure (orientation) of enzyme (molecular enzyme confirmation) - Catalysis (Type of catalysis) - According to the International Union of Biochemistry & Molecular Biology, the enzyme is described by an **enzymatic code**: - `EC X.X.X.X.` - `X` represents: - **Group Number**: [1-6] - **Sub-group**: [1-∞] - **Class**: Type of reaction - **Sub-class**: Type of substrate required co-factor ## 6 Categories of Enzymes - **1. Oxidoreductase enzymes (EC.1)** - Group of enzymes that do oxidation & reduction of two substrates at the same time. - Example: Respiration enzymes. - **2. Transferase enzyme (EC.2)** - The enzymes transfer a functional group from one substrate to another substrate. - **3- Hydrolase enzymes** - Hydrolysis of any bond of substrate using water. - **4. Lyase enzymes** - A group of enzymes (catalysis) that remove functional groups, resulting in unsaturated compounds (contain a double bond) - **5. Isomerase enzymes** - A group of enzymes that convert one compound to its isomer. - Example: - Ketone group to aldehyde group. - Double bond to single bond. - Glucose -> Fructose - **6- Ligase enzymes** - Ligation of simple molecules into large molecules. ## Example of Enzymatic Code: - `E.c. 4.1.1.11` - **Lyase**: - **Methionine** -> **Dethiolation (SH)** - **Deamination** (WH) - **Co-factor**: (vit b6) pyridoxine - **Type of substrate**: ## Enzyme Substrate Interaction - **1. Lock & key model (wrong theory)** - The enzyme combines with one absolute substrate. - **2. Induced. fit mechanism (model) (right theory)** - The active site of the enzyme and the substrate are more similar in sterioform/confirmation, the more affinity between them. ## Active Site - The binding between the active site and substrate is based on the orientation/structure/shape to fit the active site. ## Induced Fit Model - Enzyme can do re-orientation or adaptation to different substrates based on the similarities between substrates and active sites. - Chart: - Active site - S1: 100% affinity - S2: 50% affinity - S3: 0% affinity - Enzyme: - Non-active site - Alosteric site: Regulation of enzyme active site - The binding between the active site and substrate is based on the orientation/structure/shape to fit the active site.